I think, but don't quote me on this as "THE WORD," but I think that it has to do with setting up the pressure differential across the restriction.
I mean, the manifold pipes and valve openings aren't two and a quarter inches in diameter, but fitting an exhaust pipe up to that size helps anyway, right? Free flowing and all that. What I think happens, is the bigger your pipe after the restriction, the lower the pressure on that side.
As pressure differential increases across a restriction, flow increases. So if you're going for flow, you want as big a pressure differential across that restriction as possible, ideally without increasing any of the pressures involved (as that would mean you're working the engine harder just to push gases out).